Starting phenix.real_space_refine on Tue Apr 7 15:59:07 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7vam_31850/04_2026/7vam_31850.cif Found real_map, /net/cci-nas-00/data/ceres_data/7vam_31850/04_2026/7vam_31850.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7vam_31850/04_2026/7vam_31850.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7vam_31850/04_2026/7vam_31850.map" model { file = "/net/cci-nas-00/data/ceres_data/7vam_31850/04_2026/7vam_31850.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7vam_31850/04_2026/7vam_31850.cif" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.006 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians P 9 5.49 5 Mg 2 5.21 5 S 103 5.16 5 C 18735 2.51 5 N 5131 2.21 5 O 5578 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.03s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 29558 Number of models: 1 Model: "" Number of chains: 15 Chain: "A" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "B" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "C" Number of atoms: 4475 Number of conformers: 1 Conformer: "" Number of residues, atoms: 578, 4475 Classifications: {'peptide': 578} Link IDs: {'PCIS': 1, 'PTRANS': 34, 'TRANS': 542} Chain: "D" Number of atoms: 3682 Number of conformers: 1 Conformer: "" Number of residues, atoms: 470, 3682 Classifications: {'peptide': 470} Link IDs: {'PCIS': 1, 'PTRANS': 26, 'TRANS': 442} Chain: "E" Number of atoms: 3668 Number of conformers: 1 Conformer: "" Number of residues, atoms: 468, 3668 Classifications: {'peptide': 468} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 441} Chain: "F" Number of atoms: 3694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 471, 3694 Classifications: {'peptide': 471} Link IDs: {'PCIS': 1, 'PTRANS': 25, 'TRANS': 444} Chain: "G" Number of atoms: 1619 Number of conformers: 1 Conformer: "" Number of residues, atoms: 206, 1619 Classifications: {'peptide': 206} Link IDs: {'PTRANS': 9, 'TRANS': 196} Chain: "H" Number of atoms: 792 Number of conformers: 1 Conformer: "" Number of residues, atoms: 104, 792 Classifications: {'peptide': 104} Link IDs: {'PTRANS': 5, 'TRANS': 98} Chain: "I" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "J" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 976 Classifications: {'peptide': 127} Link IDs: {'PTRANS': 7, 'TRANS': 119} Chain: "K" Number of atoms: 313 Number of conformers: 1 Conformer: "" Number of residues, atoms: 40, 313 Classifications: {'peptide': 40} Link IDs: {'PTRANS': 1, 'TRANS': 38} Chain: "L" Number of atoms: 980 Number of conformers: 1 Conformer: "" Number of residues, atoms: 128, 980 Classifications: {'peptide': 128} Link IDs: {'PTRANS': 7, 'TRANS': 120} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 1, 'ADP': 1, 'PO4': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 31 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 31 Unusual residues: {'ATP': 1} Classifications: {'undetermined': 1} Chain: "C" Number of atoms: 32 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 32 Unusual residues: {' MG': 1, 'ATP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 5.97, per 1000 atoms: 0.20 Number of scatterers: 29558 At special positions: 0 Unit cell: (149.6, 147.84, 177.76, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 103 16.00 P 9 15.00 Mg 2 11.99 O 5578 8.00 N 5131 7.00 C 18735 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.26 Conformation dependent library (CDL) restraints added in 1.3 seconds 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 6918 Finding SS restraints... Secondary structure from input PDB file: 146 helices and 27 sheets defined 47.3% alpha, 10.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 90 through 99 Processing helix chain 'A' and resid 209 through 215 Processing helix chain 'A' and resid 233 through 244 Processing helix chain 'A' and resid 258 through 269 removed outlier: 3.876A pdb=" N VAL A 265 " --> pdb=" O GLU A 261 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N LEU A 266 " --> pdb=" O MET A 262 " (cutoff:3.500A) Processing helix chain 'A' and resid 270 through 272 No H-bonds generated for 'chain 'A' and resid 270 through 272' Processing helix chain 'A' and resid 280 through 283 Processing helix chain 'A' and resid 295 through 316 removed outlier: 4.448A pdb=" N ILE A 303 " --> pdb=" O ARG A 299 " (cutoff:3.500A) removed outlier: 4.510A pdb=" N TYR A 304 " --> pdb=" O GLU A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 327 through 342 removed outlier: 3.755A pdb=" N ALA A 333 " --> pdb=" O ARG A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 353 through 363 Processing helix chain 'A' and resid 386 through 390 Processing helix chain 'A' and resid 393 through 401 Processing helix chain 'A' and resid 410 through 416 Processing helix chain 'A' and resid 431 through 443 Proline residue: A 437 - end of helix removed outlier: 3.544A pdb=" N GLU A 441 " --> pdb=" O PRO A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 446 through 472 removed outlier: 3.912A pdb=" N GLU A 466 " --> pdb=" O ALA A 462 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N ILE A 467 " --> pdb=" O GLY A 463 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 removed outlier: 3.500A pdb=" N LEU A 476 " --> pdb=" O PRO A 473 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 477 through 494 Processing helix chain 'A' and resid 508 through 532 Processing helix chain 'A' and resid 538 through 542 removed outlier: 3.750A pdb=" N GLN A 541 " --> pdb=" O GLU A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 543 through 550 removed outlier: 3.928A pdb=" N ARG A 547 " --> pdb=" O PRO A 543 " (cutoff:3.500A) Processing helix chain 'A' and resid 558 through 578 removed outlier: 3.890A pdb=" N GLU A 564 " --> pdb=" O PRO A 560 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N PHE A 574 " --> pdb=" O ILE A 570 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 575 " --> pdb=" O GLN A 571 " (cutoff:3.500A) Processing helix chain 'B' and resid 90 through 99 Processing helix chain 'B' and resid 209 through 215 Processing helix chain 'B' and resid 233 through 245 Processing helix chain 'B' and resid 258 through 269 Processing helix chain 'B' and resid 270 through 272 No H-bonds generated for 'chain 'B' and resid 270 through 272' Processing helix chain 'B' and resid 280 through 283 Processing helix chain 'B' and resid 295 through 316 removed outlier: 4.664A pdb=" N ILE B 303 " --> pdb=" O ARG B 299 " (cutoff:3.500A) removed outlier: 4.814A pdb=" N TYR B 304 " --> pdb=" O GLU B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 326 through 341 removed outlier: 3.622A pdb=" N TRP B 330 " --> pdb=" O SER B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 353 through 363 Processing helix chain 'B' and resid 393 through 401 Processing helix chain 'B' and resid 410 through 416 removed outlier: 3.793A pdb=" N ALA B 414 " --> pdb=" O ASP B 410 " (cutoff:3.500A) Processing helix chain 'B' and resid 431 through 443 Proline residue: B 437 - end of helix Processing helix chain 'B' and resid 446 through 463 Processing helix chain 'B' and resid 464 through 472 removed outlier: 3.525A pdb=" N VAL B 468 " --> pdb=" O LEU B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 477 through 494 Processing helix chain 'B' and resid 508 through 532 Processing helix chain 'B' and resid 535 through 540 Processing helix chain 'B' and resid 542 through 550 removed outlier: 4.133A pdb=" N GLU B 546 " --> pdb=" O LEU B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 577 removed outlier: 3.616A pdb=" N PHE B 574 " --> pdb=" O ILE B 570 " (cutoff:3.500A) removed outlier: 4.185A pdb=" N LYS B 575 " --> pdb=" O GLN B 571 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 99 Processing helix chain 'C' and resid 209 through 215 Processing helix chain 'C' and resid 233 through 244 Processing helix chain 'C' and resid 258 through 269 removed outlier: 3.893A pdb=" N MET C 262 " --> pdb=" O ARG C 258 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N VAL C 265 " --> pdb=" O GLU C 261 " (cutoff:3.500A) Processing helix chain 'C' and resid 270 through 272 No H-bonds generated for 'chain 'C' and resid 270 through 272' Processing helix chain 'C' and resid 280 through 283 Processing helix chain 'C' and resid 297 through 316 removed outlier: 3.912A pdb=" N ALA C 301 " --> pdb=" O ALA C 297 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N ILE C 303 " --> pdb=" O ARG C 299 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N TYR C 304 " --> pdb=" O GLU C 300 " (cutoff:3.500A) Processing helix chain 'C' and resid 326 through 341 removed outlier: 4.087A pdb=" N TRP C 330 " --> pdb=" O SER C 326 " (cutoff:3.500A) Processing helix chain 'C' and resid 353 through 363 Processing helix chain 'C' and resid 386 through 390 Processing helix chain 'C' and resid 393 through 401 removed outlier: 3.604A pdb=" N ARG C 401 " --> pdb=" O GLN C 397 " (cutoff:3.500A) Processing helix chain 'C' and resid 410 through 416 Processing helix chain 'C' and resid 432 through 434 No H-bonds generated for 'chain 'C' and resid 432 through 434' Processing helix chain 'C' and resid 435 through 443 Processing helix chain 'C' and resid 446 through 472 removed outlier: 3.954A pdb=" N GLU C 466 " --> pdb=" O ALA C 462 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ILE C 467 " --> pdb=" O GLY C 463 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N LEU C 470 " --> pdb=" O GLU C 466 " (cutoff:3.500A) Processing helix chain 'C' and resid 477 through 494 Processing helix chain 'C' and resid 508 through 532 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.566A pdb=" N ILE C 539 " --> pdb=" O SER C 535 " (cutoff:3.500A) Processing helix chain 'C' and resid 543 through 550 removed outlier: 3.708A pdb=" N ARG C 547 " --> pdb=" O PRO C 543 " (cutoff:3.500A) Processing helix chain 'C' and resid 551 through 554 Processing helix chain 'C' and resid 558 through 574 removed outlier: 3.904A pdb=" N PHE C 574 " --> pdb=" O ILE C 570 " (cutoff:3.500A) Processing helix chain 'C' and resid 575 through 578 Processing helix chain 'D' and resid 85 through 89 removed outlier: 3.864A pdb=" N LEU D 89 " --> pdb=" O LYS D 86 " (cutoff:3.500A) Processing helix chain 'D' and resid 120 through 124 Processing helix chain 'D' and resid 135 through 142 removed outlier: 3.561A pdb=" N MET D 141 " --> pdb=" O THR D 137 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 171 removed outlier: 3.525A pdb=" N ILE D 163 " --> pdb=" O PRO D 159 " (cutoff:3.500A) Processing helix chain 'D' and resid 174 through 179 Processing helix chain 'D' and resid 197 through 212 removed outlier: 3.942A pdb=" N THR D 211 " --> pdb=" O GLU D 207 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N GLY D 212 " --> pdb=" O PHE D 208 " (cutoff:3.500A) Processing helix chain 'D' and resid 213 through 215 No H-bonds generated for 'chain 'D' and resid 213 through 215' Processing helix chain 'D' and resid 227 through 250 Proline residue: D 235 - end of helix Processing helix chain 'D' and resid 259 through 274 Processing helix chain 'D' and resid 279 through 283 Processing helix chain 'D' and resid 286 through 296 removed outlier: 3.504A pdb=" N ILE D 294 " --> pdb=" O ASP D 290 " (cutoff:3.500A) Processing helix chain 'D' and resid 323 through 333 Processing helix chain 'D' and resid 340 through 346 Processing helix chain 'D' and resid 361 through 365 Processing helix chain 'D' and resid 374 through 400 removed outlier: 3.866A pdb=" N ASP D 391 " --> pdb=" O ALA D 387 " (cutoff:3.500A) removed outlier: 3.702A pdb=" N ILE D 392 " --> pdb=" O ASN D 388 " (cutoff:3.500A) removed outlier: 3.556A pdb=" N LYS D 394 " --> pdb=" O VAL D 390 " (cutoff:3.500A) removed outlier: 4.128A pdb=" N ALA D 397 " --> pdb=" O ARG D 393 " (cutoff:3.500A) removed outlier: 4.016A pdb=" N ILE D 398 " --> pdb=" O LYS D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 401 through 404 Processing helix chain 'D' and resid 405 through 422 removed outlier: 3.518A pdb=" N ARG D 409 " --> pdb=" O THR D 405 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ARG D 410 " --> pdb=" O GLU D 406 " (cutoff:3.500A) Processing helix chain 'D' and resid 431 through 444 Processing helix chain 'D' and resid 455 through 463 Processing helix chain 'D' and resid 467 through 472 removed outlier: 4.313A pdb=" N TRP D 471 " --> pdb=" O LEU D 467 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 89 Processing helix chain 'E' and resid 135 through 140 Processing helix chain 'E' and resid 159 through 171 Processing helix chain 'E' and resid 174 through 179 removed outlier: 3.908A pdb=" N SER E 178 " --> pdb=" O ARG E 174 " (cutoff:3.500A) Processing helix chain 'E' and resid 197 through 212 Processing helix chain 'E' and resid 213 through 215 No H-bonds generated for 'chain 'E' and resid 213 through 215' Processing helix chain 'E' and resid 228 through 231 Processing helix chain 'E' and resid 232 through 250 removed outlier: 4.482A pdb=" N ARG E 236 " --> pdb=" O ILE E 232 " (cutoff:3.500A) Processing helix chain 'E' and resid 259 through 275 removed outlier: 3.669A pdb=" N TYR E 263 " --> pdb=" O ASP E 259 " (cutoff:3.500A) Processing helix chain 'E' and resid 286 through 296 removed outlier: 3.604A pdb=" N ILE E 294 " --> pdb=" O ASP E 290 " (cutoff:3.500A) Processing helix chain 'E' and resid 317 through 320 Processing helix chain 'E' and resid 323 through 331 Processing helix chain 'E' and resid 340 through 346 removed outlier: 3.507A pdb=" N HIS E 344 " --> pdb=" O SER E 340 " (cutoff:3.500A) Processing helix chain 'E' and resid 361 through 366 removed outlier: 3.969A pdb=" N GLY E 365 " --> pdb=" O LEU E 361 " (cutoff:3.500A) Processing helix chain 'E' and resid 374 through 400 removed outlier: 4.136A pdb=" N ILE E 398 " --> pdb=" O LYS E 394 " (cutoff:3.500A) Processing helix chain 'E' and resid 401 through 404 Processing helix chain 'E' and resid 405 through 422 Processing helix chain 'E' and resid 431 through 444 Processing helix chain 'E' and resid 445 through 446 No H-bonds generated for 'chain 'E' and resid 445 through 446' Processing helix chain 'E' and resid 447 through 451 Processing helix chain 'E' and resid 455 through 463 Processing helix chain 'E' and resid 466 through 470 removed outlier: 3.838A pdb=" N GLU E 469 " --> pdb=" O LYS E 466 " (cutoff:3.500A) Processing helix chain 'F' and resid 85 through 89 removed outlier: 3.541A pdb=" N MET F 88 " --> pdb=" O SER F 85 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU F 89 " --> pdb=" O LYS F 86 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 85 through 89' Processing helix chain 'F' and resid 120 through 124 Processing helix chain 'F' and resid 135 through 140 Processing helix chain 'F' and resid 159 through 171 removed outlier: 3.566A pdb=" N ILE F 163 " --> pdb=" O PRO F 159 " (cutoff:3.500A) Processing helix chain 'F' and resid 174 through 179 Processing helix chain 'F' and resid 197 through 212 Processing helix chain 'F' and resid 213 through 215 No H-bonds generated for 'chain 'F' and resid 213 through 215' Processing helix chain 'F' and resid 227 through 232 Processing helix chain 'F' and resid 233 through 250 Processing helix chain 'F' and resid 259 through 274 removed outlier: 3.703A pdb=" N TYR F 263 " --> pdb=" O ASP F 259 " (cutoff:3.500A) Processing helix chain 'F' and resid 286 through 296 removed outlier: 3.563A pdb=" N ILE F 294 " --> pdb=" O ASP F 290 " (cutoff:3.500A) Processing helix chain 'F' and resid 317 through 320 Processing helix chain 'F' and resid 323 through 333 Processing helix chain 'F' and resid 340 through 346 Processing helix chain 'F' and resid 361 through 366 removed outlier: 3.955A pdb=" N GLY F 365 " --> pdb=" O LEU F 361 " (cutoff:3.500A) removed outlier: 3.619A pdb=" N VAL F 366 " --> pdb=" O MET F 362 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 361 through 366' Processing helix chain 'F' and resid 374 through 400 removed outlier: 3.765A pdb=" N ILE F 398 " --> pdb=" O LYS F 394 " (cutoff:3.500A) Processing helix chain 'F' and resid 401 through 404 Processing helix chain 'F' and resid 405 through 422 Processing helix chain 'F' and resid 431 through 444 Processing helix chain 'F' and resid 445 through 446 No H-bonds generated for 'chain 'F' and resid 445 through 446' Processing helix chain 'F' and resid 447 through 451 removed outlier: 3.649A pdb=" N LEU F 451 " --> pdb=" O GLN F 448 " (cutoff:3.500A) Processing helix chain 'F' and resid 455 through 463 Processing helix chain 'F' and resid 466 through 471 removed outlier: 3.897A pdb=" N ILE F 470 " --> pdb=" O LYS F 466 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N TRP F 471 " --> pdb=" O LEU F 467 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 466 through 471' Processing helix chain 'G' and resid 7 through 68 removed outlier: 3.741A pdb=" N GLU G 48 " --> pdb=" O ARG G 44 " (cutoff:3.500A) Processing helix chain 'G' and resid 122 through 207 removed outlier: 4.566A pdb=" N ARG G 128 " --> pdb=" O LEU G 124 " (cutoff:3.500A) removed outlier: 5.328A pdb=" N ILE G 169 " --> pdb=" O GLU G 165 " (cutoff:3.500A) Proline residue: G 170 - end of helix Processing helix chain 'H' and resid 8 through 15 removed outlier: 3.834A pdb=" N GLY H 12 " --> pdb=" O GLU H 8 " (cutoff:3.500A) Processing helix chain 'H' and resid 25 through 38 Processing helix chain 'H' and resid 54 through 59 removed outlier: 3.736A pdb=" N ARG H 57 " --> pdb=" O ASP H 54 " (cutoff:3.500A) Processing helix chain 'H' and resid 85 through 99 Processing helix chain 'I' and resid 82 through 104 removed outlier: 3.811A pdb=" N LYS I 97 " --> pdb=" O GLU I 93 " (cutoff:3.500A) removed outlier: 4.374A pdb=" N ARG I 100 " --> pdb=" O ALA I 96 " (cutoff:3.500A) Processing helix chain 'I' and resid 106 through 119 removed outlier: 3.562A pdb=" N GLU I 117 " --> pdb=" O LEU I 113 " (cutoff:3.500A) Processing helix chain 'J' and resid 62 through 92 Processing helix chain 'J' and resid 99 through 115 removed outlier: 3.854A pdb=" N VAL J 103 " --> pdb=" O GLU J 99 " (cutoff:3.500A) removed outlier: 3.936A pdb=" N ARG J 105 " --> pdb=" O PRO J 101 " (cutoff:3.500A) Processing helix chain 'J' and resid 124 through 126 No H-bonds generated for 'chain 'J' and resid 124 through 126' Processing helix chain 'J' and resid 127 through 139 removed outlier: 4.914A pdb=" N ALA J 133 " --> pdb=" O PRO J 129 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ARG J 136 " --> pdb=" O GLU J 132 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ARG J 138 " --> pdb=" O LEU J 134 " (cutoff:3.500A) Processing helix chain 'J' and resid 146 through 149 Processing helix chain 'J' and resid 166 through 187 removed outlier: 5.480A pdb=" N ASP J 176 " --> pdb=" O ASP J 172 " (cutoff:3.500A) removed outlier: 5.676A pdb=" N ALA J 177 " --> pdb=" O ARG J 173 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N ALA J 183 " --> pdb=" O SER J 179 " (cutoff:3.500A) removed outlier: 4.337A pdb=" N GLN J 184 " --> pdb=" O SER J 180 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N ALA J 185 " --> pdb=" O LYS J 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 82 through 105 removed outlier: 3.790A pdb=" N ALA K 105 " --> pdb=" O GLU K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 106 through 119 Processing helix chain 'L' and resid 62 through 93 removed outlier: 3.691A pdb=" N LEU L 67 " --> pdb=" O ALA L 63 " (cutoff:3.500A) removed outlier: 3.630A pdb=" N VAL L 68 " --> pdb=" O GLY L 64 " (cutoff:3.500A) Processing helix chain 'L' and resid 99 through 115 removed outlier: 3.869A pdb=" N ARG L 105 " --> pdb=" O PRO L 101 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N LYS L 106 " --> pdb=" O GLU L 102 " (cutoff:3.500A) Processing helix chain 'L' and resid 127 through 139 removed outlier: 4.466A pdb=" N ALA L 133 " --> pdb=" O PRO L 129 " (cutoff:3.500A) removed outlier: 4.236A pdb=" N LEU L 134 " --> pdb=" O HIS L 130 " (cutoff:3.500A) Processing helix chain 'L' and resid 167 through 188 removed outlier: 3.677A pdb=" N ASP L 172 " --> pdb=" O LEU L 168 " (cutoff:3.500A) removed outlier: 4.683A pdb=" N ASP L 176 " --> pdb=" O ASP L 172 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N ALA L 177 " --> pdb=" O ARG L 173 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N SER L 180 " --> pdb=" O ASP L 176 " (cutoff:3.500A) removed outlier: 4.626A pdb=" N LYS L 181 " --> pdb=" O ALA L 177 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 3 through 10 removed outlier: 6.584A pdb=" N ILE A 15 " --> pdb=" O GLN A 7 " (cutoff:3.500A) removed outlier: 5.010A pdb=" N ILE A 9 " --> pdb=" O ALA A 13 " (cutoff:3.500A) removed outlier: 7.332A pdb=" N ALA A 13 " --> pdb=" O ILE A 9 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 13 through 17 current: chain 'A' and resid 35 through 43 removed outlier: 5.537A pdb=" N ILE A 39 " --> pdb=" O GLN A 50 " (cutoff:3.500A) removed outlier: 6.427A pdb=" N GLN A 50 " --> pdb=" O ILE A 39 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ARG A 41 " --> pdb=" O PHE A 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 46 through 51 current: chain 'B' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 13 through 17 current: chain 'B' and resid 35 through 43 removed outlier: 6.631A pdb=" N PHE B 48 " --> pdb=" O ILE B 40 " (cutoff:3.500A) removed outlier: 4.647A pdb=" N LEU B 42 " --> pdb=" O THR B 46 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N THR B 46 " --> pdb=" O LEU B 42 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 46 through 51 current: chain 'C' and resid 13 through 17 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 13 through 17 current: chain 'C' and resid 35 through 43 removed outlier: 5.750A pdb=" N ILE C 39 " --> pdb=" O GLN C 50 " (cutoff:3.500A) removed outlier: 6.802A pdb=" N GLN C 50 " --> pdb=" O ILE C 39 " (cutoff:3.500A) removed outlier: 3.786A pdb=" N ARG C 41 " --> pdb=" O PHE C 48 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 46 through 51 current: chain 'D' and resid 18 through 22 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 18 through 22 current: chain 'D' and resid 42 through 51 removed outlier: 6.628A pdb=" N VAL D 56 " --> pdb=" O ILE D 48 " (cutoff:3.500A) removed outlier: 5.062A pdb=" N VAL D 50 " --> pdb=" O TYR D 54 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR D 54 " --> pdb=" O VAL D 50 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 54 through 59 current: chain 'E' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 18 through 21 current: chain 'E' and resid 42 through 51 removed outlier: 5.683A pdb=" N VAL E 47 " --> pdb=" O GLN E 58 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N GLN E 58 " --> pdb=" O VAL E 47 " (cutoff:3.500A) removed outlier: 3.541A pdb=" N GLU E 49 " --> pdb=" O VAL E 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 55 through 59 current: chain 'F' and resid 18 through 21 WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 18 through 21 current: chain 'F' and resid 42 through 51 removed outlier: 5.741A pdb=" N VAL F 47 " --> pdb=" O GLN F 58 " (cutoff:3.500A) removed outlier: 6.560A pdb=" N GLN F 58 " --> pdb=" O VAL F 47 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLU F 49 " --> pdb=" O VAL F 56 " (cutoff:3.500A) WARNING: can't find start of bonding for strands! previous: chain 'F' and resid 55 through 59 current: chain 'J' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 141 through 144 current: chain 'J' and resid 161 through 164 WARNING: can't find start of bonding for strands! previous: chain 'J' and resid 161 through 164 current: chain 'L' and resid 141 through 144 WARNING: can't find start of bonding for strands! previous: chain 'L' and resid 141 through 144 current: chain 'L' and resid 161 through 166 Processing sheet with id=AA2, first strand: chain 'A' and resid 72 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 82 through 84 current: chain 'A' and resid 285 through 291 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 285 through 291 current: chain 'A' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'A' and resid 375 through 384 current: chain 'A' and resid 428 through 429 No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 117 through 119 removed outlier: 3.738A pdb=" N GLY A 164 " --> pdb=" O TRP A 119 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 128 through 129 removed outlier: 6.895A pdb=" N VAL A 174 " --> pdb=" O LYS A 158 " (cutoff:3.500A) removed outlier: 3.599A pdb=" N VAL A 173 " --> pdb=" O LEU A 181 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 134 through 140 removed outlier: 3.948A pdb=" N GLY A 136 " --> pdb=" O ILE A 147 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 72 through 75 Processing sheet with id=AA8, first strand: chain 'B' and resid 83 through 84 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 83 through 84 current: chain 'B' and resid 285 through 288 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 285 through 288 current: chain 'B' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'B' and resid 375 through 384 current: chain 'B' and resid 428 through 429 No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'B' and resid 143 through 148 removed outlier: 6.355A pdb=" N PHE B 143 " --> pdb=" O PRO B 139 " (cutoff:3.500A) removed outlier: 6.478A pdb=" N HIS B 145 " --> pdb=" O THR B 137 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N THR B 137 " --> pdb=" O HIS B 145 " (cutoff:3.500A) removed outlier: 6.667A pdb=" N ILE B 147 " --> pdb=" O LEU B 135 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ALA B 118 " --> pdb=" O PRO B 139 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 128 through 130 removed outlier: 6.659A pdb=" N VAL B 174 " --> pdb=" O LYS B 158 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'C' and resid 72 through 75 Processing sheet with id=AB3, first strand: chain 'C' and resid 82 through 84 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 82 through 84 current: chain 'C' and resid 285 through 290 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 285 through 290 current: chain 'C' and resid 375 through 384 WARNING: can't find start of bonding for strands! previous: chain 'C' and resid 375 through 384 current: chain 'C' and resid 428 through 429 No H-bonds generated for sheet with id=AB3 Processing sheet with id=AB4, first strand: chain 'C' and resid 143 through 148 removed outlier: 6.515A pdb=" N PHE C 143 " --> pdb=" O PRO C 139 " (cutoff:3.500A) removed outlier: 6.482A pdb=" N HIS C 145 " --> pdb=" O THR C 137 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N THR C 137 " --> pdb=" O HIS C 145 " (cutoff:3.500A) removed outlier: 6.588A pdb=" N ILE C 147 " --> pdb=" O LEU C 135 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ALA C 118 " --> pdb=" O PRO C 139 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'C' and resid 128 through 129 removed outlier: 3.731A pdb=" N GLY C 155 " --> pdb=" O VAL C 129 " (cutoff:3.500A) removed outlier: 6.975A pdb=" N VAL C 174 " --> pdb=" O LYS C 158 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'D' and resid 81 through 84 removed outlier: 3.644A pdb=" N LYS D 110 " --> pdb=" O VAL D 84 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'D' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 92 through 93 current: chain 'D' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 217 through 223 current: chain 'D' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'D' and resid 307 through 315 current: chain 'D' and resid 358 through 359 No H-bonds generated for sheet with id=AB7 Processing sheet with id=AB8, first strand: chain 'D' and resid 130 through 131 removed outlier: 4.730A pdb=" N LEU D 144 " --> pdb=" O ILE D 131 " (cutoff:3.500A) Processing sheet with id=AB9, first strand: chain 'E' and resid 81 through 84 Processing sheet with id=AC1, first strand: chain 'E' and resid 92 through 93 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 92 through 93 current: chain 'E' and resid 217 through 223 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 217 through 223 current: chain 'E' and resid 307 through 315 WARNING: can't find start of bonding for strands! previous: chain 'E' and resid 307 through 315 current: chain 'E' and resid 358 through 359 No H-bonds generated for sheet with id=AC1 Processing sheet with id=AC2, first strand: chain 'E' and resid 130 through 131 removed outlier: 4.623A pdb=" N LEU E 144 " --> pdb=" O ILE E 131 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'F' and resid 81 through 84 Processing sheet with id=AC4, first strand: chain 'F' and resid 92 through 94 removed outlier: 6.349A pdb=" N ALA F 188 " --> pdb=" O LEU F 254 " (cutoff:3.500A) removed outlier: 7.787A pdb=" N ILE F 256 " --> pdb=" O ALA F 188 " (cutoff:3.500A) removed outlier: 6.805A pdb=" N VAL F 190 " --> pdb=" O ILE F 256 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N LEU F 257 " --> pdb=" O ILE F 311 " (cutoff:3.500A) Processing sheet with id=AC5, first strand: chain 'F' and resid 131 through 132 Processing sheet with id=AC6, first strand: chain 'F' and resid 278 through 280 removed outlier: 6.419A pdb=" N TYR F 283 " --> pdb=" O GLY F 279 " (cutoff:3.500A) Processing sheet with id=AC7, first strand: chain 'G' and resid 90 through 91 removed outlier: 4.008A pdb=" N GLU G 90 " --> pdb=" O LYS G 105 " (cutoff:3.500A) Processing sheet with id=AC8, first strand: chain 'G' and resid 94 through 96 Processing sheet with id=AC9, first strand: chain 'H' and resid 19 through 22 removed outlier: 7.632A pdb=" N ILE H 74 " --> pdb=" O VAL H 45 " (cutoff:3.500A) removed outlier: 6.407A pdb=" N VAL H 47 " --> pdb=" O ILE H 74 " (cutoff:3.500A) 1247 hydrogen bonds defined for protein. 3558 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 5.34 Time building geometry restraints manager: 3.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 9948 1.34 - 1.46: 3814 1.46 - 1.57: 16145 1.57 - 1.69: 13 1.69 - 1.80: 194 Bond restraints: 30114 Sorted by residual: bond pdb=" C4 ATP B 601 " pdb=" C5 ATP B 601 " ideal model delta sigma weight residual 1.388 1.461 -0.073 1.00e-02 1.00e+04 5.28e+01 bond pdb=" C4 ATP C 601 " pdb=" C5 ATP C 601 " ideal model delta sigma weight residual 1.388 1.454 -0.066 1.00e-02 1.00e+04 4.36e+01 bond pdb=" C5 ATP B 601 " pdb=" C6 ATP B 601 " ideal model delta sigma weight residual 1.409 1.475 -0.066 1.00e-02 1.00e+04 4.33e+01 bond pdb=" C5 ATP C 601 " pdb=" C6 ATP C 601 " ideal model delta sigma weight residual 1.409 1.469 -0.060 1.00e-02 1.00e+04 3.58e+01 bond pdb=" C5 ATP C 601 " pdb=" N7 ATP C 601 " ideal model delta sigma weight residual 1.387 1.337 0.050 1.00e-02 1.00e+04 2.46e+01 ... (remaining 30109 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.70: 40703 3.70 - 7.41: 96 7.41 - 11.11: 9 11.11 - 14.82: 2 14.82 - 18.52: 3 Bond angle restraints: 40813 Sorted by residual: angle pdb=" PB ATP C 601 " pdb=" O3B ATP C 601 " pdb=" PG ATP C 601 " ideal model delta sigma weight residual 139.87 121.35 18.52 1.00e+00 1.00e+00 3.43e+02 angle pdb=" PB ATP B 601 " pdb=" O3B ATP B 601 " pdb=" PG ATP B 601 " ideal model delta sigma weight residual 139.87 121.58 18.29 1.00e+00 1.00e+00 3.35e+02 angle pdb=" PA ATP C 601 " pdb=" O3A ATP C 601 " pdb=" PB ATP C 601 " ideal model delta sigma weight residual 136.83 120.29 16.54 1.00e+00 1.00e+00 2.74e+02 angle pdb=" PA ATP B 601 " pdb=" O3A ATP B 601 " pdb=" PB ATP B 601 " ideal model delta sigma weight residual 136.83 122.06 14.77 1.00e+00 1.00e+00 2.18e+02 angle pdb=" C5 ATP B 601 " pdb=" C4 ATP B 601 " pdb=" N3 ATP B 601 " ideal model delta sigma weight residual 126.80 118.38 8.42 1.00e+00 1.00e+00 7.08e+01 ... (remaining 40808 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 24.83: 17538 24.83 - 49.65: 722 49.65 - 74.48: 92 74.48 - 99.31: 30 99.31 - 124.13: 1 Dihedral angle restraints: 18383 sinusoidal: 7561 harmonic: 10822 Sorted by residual: dihedral pdb=" O1B ADP A 601 " pdb=" O3A ADP A 601 " pdb=" PB ADP A 601 " pdb=" PA ADP A 601 " ideal model delta sinusoidal sigma weight residual 300.00 175.86 124.13 1 2.00e+01 2.50e-03 3.75e+01 dihedral pdb=" C5' ADP A 601 " pdb=" O5' ADP A 601 " pdb=" PA ADP A 601 " pdb=" O2A ADP A 601 " ideal model delta sinusoidal sigma weight residual -60.00 32.58 -92.58 1 2.00e+01 2.50e-03 2.51e+01 dihedral pdb=" CA ARG A 23 " pdb=" C ARG A 23 " pdb=" N MET A 24 " pdb=" CA MET A 24 " ideal model delta harmonic sigma weight residual 180.00 -160.06 -19.94 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 18380 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.287: 4571 0.287 - 0.574: 0 0.574 - 0.861: 0 0.861 - 1.148: 0 1.148 - 1.436: 1 Chirality restraints: 4572 Sorted by residual: chirality pdb=" C4' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" C5' ATP B 601 " pdb=" O4' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.49 -1.06 -1.44 2.00e-01 2.50e+01 5.15e+01 chirality pdb=" CB ILE B 211 " pdb=" CA ILE B 211 " pdb=" CG1 ILE B 211 " pdb=" CG2 ILE B 211 " both_signs ideal model delta sigma weight residual False 2.64 2.36 0.28 2.00e-01 2.50e+01 1.98e+00 chirality pdb=" C2' ATP B 601 " pdb=" C1' ATP B 601 " pdb=" C3' ATP B 601 " pdb=" O2' ATP B 601 " both_signs ideal model delta sigma weight residual False -2.68 -2.51 -0.17 2.00e-01 2.50e+01 7.33e-01 ... (remaining 4569 not shown) Planarity restraints: 5333 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL G 101 " 0.030 5.00e-02 4.00e+02 4.51e-02 3.25e+00 pdb=" N PRO G 102 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO G 102 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO G 102 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE B 226 " 0.025 5.00e-02 4.00e+02 3.81e-02 2.32e+00 pdb=" N PRO B 227 " -0.066 5.00e-02 4.00e+02 pdb=" CA PRO B 227 " 0.020 5.00e-02 4.00e+02 pdb=" CD PRO B 227 " 0.021 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS E 323 " 0.025 5.00e-02 4.00e+02 3.78e-02 2.28e+00 pdb=" N PRO E 324 " -0.065 5.00e-02 4.00e+02 pdb=" CA PRO E 324 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 324 " 0.021 5.00e-02 4.00e+02 ... (remaining 5330 not shown) Histogram of nonbonded interaction distances: 1.63 - 2.29: 12 2.29 - 2.94: 12579 2.94 - 3.59: 42431 3.59 - 4.25: 67502 4.25 - 4.90: 116773 Nonbonded interactions: 239297 Sorted by model distance: nonbonded pdb=" OG SER A 235 " pdb="MG MG A 602 " model vdw 1.634 2.170 nonbonded pdb=" O LEU B 241 " pdb=" OG SER B 245 " model vdw 2.146 3.040 nonbonded pdb=" O MET C 220 " pdb=" OG1 THR C 379 " model vdw 2.147 3.040 nonbonded pdb=" O MET A 220 " pdb=" OG1 THR A 379 " model vdw 2.160 3.040 nonbonded pdb=" OG1 THR C 167 " pdb=" OE1 GLU C 170 " model vdw 2.163 3.040 ... (remaining 239292 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 1 through 578) selection = (chain 'B' and resid 1 through 578) selection = (chain 'C' and resid 1 through 578) } ncs_group { reference = (chain 'D' and resid 5 through 470) selection = (chain 'E' and resid 5 through 470) selection = (chain 'F' and resid 5 through 470) } ncs_group { reference = chain 'I' selection = chain 'K' } ncs_group { reference = chain 'J' selection = (chain 'L' and resid 61 through 187) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.040 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.080 Process input model: 25.290 Find NCS groups from input model: 0.610 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.200 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.073 30114 Z= 0.189 Angle : 0.608 18.521 40813 Z= 0.377 Chirality : 0.048 1.436 4572 Planarity : 0.004 0.045 5333 Dihedral : 13.552 124.132 11465 Min Nonbonded Distance : 1.634 Molprobity Statistics. All-atom Clashscore : 3.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.41 % Favored : 98.59 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.25 (0.14), residues: 3764 helix: 1.70 (0.14), residues: 1560 sheet: 0.14 (0.21), residues: 643 loop : 0.39 (0.16), residues: 1561 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 364 TYR 0.014 0.001 TYR E 13 PHE 0.012 0.001 PHE C 406 TRP 0.012 0.001 TRP L 100 HIS 0.002 0.001 HIS L 130 Details of bonding type rmsd covalent geometry : bond 0.00350 (30114) covalent geometry : angle 0.60780 (40813) hydrogen bonds : bond 0.15808 ( 1247) hydrogen bonds : angle 5.69247 ( 3558) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 545 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 545 time to evaluate : 0.825 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 17 LYS cc_start: 0.8088 (ptmm) cc_final: 0.7748 (pttp) REVERT: A 24 MET cc_start: 0.7983 (tpt) cc_final: 0.7606 (tpt) REVERT: A 74 GLU cc_start: 0.8482 (mt-10) cc_final: 0.8085 (mt-10) REVERT: A 124 LYS cc_start: 0.7217 (mptt) cc_final: 0.6892 (mmtm) REVERT: A 300 GLU cc_start: 0.7555 (tm-30) cc_final: 0.7073 (tp30) REVERT: A 329 ARG cc_start: 0.4982 (mtm-85) cc_final: 0.4427 (mmp80) REVERT: A 330 TRP cc_start: 0.7857 (t60) cc_final: 0.7626 (t60) REVERT: A 347 GLU cc_start: 0.6473 (tt0) cc_final: 0.5854 (pm20) REVERT: A 456 GLU cc_start: 0.7314 (tt0) cc_final: 0.6659 (mt-10) REVERT: A 469 GLN cc_start: 0.7255 (mm-40) cc_final: 0.6967 (mt0) REVERT: A 527 GLU cc_start: 0.7151 (mm-30) cc_final: 0.6940 (mm-30) REVERT: A 550 ARG cc_start: 0.7181 (mmt180) cc_final: 0.6955 (mmm160) REVERT: A 569 GLU cc_start: 0.5446 (tt0) cc_final: 0.4991 (mm-30) REVERT: B 124 LYS cc_start: 0.5667 (mmtm) cc_final: 0.5374 (mtpp) REVERT: B 133 MET cc_start: 0.7708 (mtp) cc_final: 0.7445 (mtm) REVERT: B 172 VAL cc_start: 0.8319 (t) cc_final: 0.7947 (m) REVERT: B 197 ARG cc_start: 0.7760 (ttp-110) cc_final: 0.7396 (ttp-110) REVERT: B 257 GLU cc_start: 0.7399 (mm-30) cc_final: 0.7048 (mm-30) REVERT: B 363 GLU cc_start: 0.7435 (mm-30) cc_final: 0.6938 (mm-30) REVERT: B 441 GLU cc_start: 0.6392 (tp30) cc_final: 0.6164 (tt0) REVERT: B 474 ASP cc_start: 0.6454 (t0) cc_final: 0.5981 (p0) REVERT: B 485 GLU cc_start: 0.7176 (mm-30) cc_final: 0.6899 (mm-30) REVERT: B 489 ILE cc_start: 0.6341 (mt) cc_final: 0.6128 (mt) REVERT: B 506 TYR cc_start: 0.7182 (t80) cc_final: 0.6892 (t80) REVERT: B 520 LEU cc_start: 0.7320 (mm) cc_final: 0.7025 (mm) REVERT: B 524 LYS cc_start: 0.5185 (mtmt) cc_final: 0.4759 (tttm) REVERT: C 124 LYS cc_start: 0.7360 (ptpp) cc_final: 0.6380 (mttm) REVERT: C 130 ARG cc_start: 0.7313 (mtm180) cc_final: 0.7102 (mtp85) REVERT: C 156 ARG cc_start: 0.7540 (ttp-170) cc_final: 0.7213 (ttt-90) REVERT: C 160 VAL cc_start: 0.8777 (t) cc_final: 0.8507 (m) REVERT: C 220 MET cc_start: 0.7736 (mmt) cc_final: 0.7402 (tpt) REVERT: C 441 GLU cc_start: 0.6811 (mt-10) cc_final: 0.6573 (tt0) REVERT: C 481 ARG cc_start: 0.6402 (mtp85) cc_final: 0.6123 (ttt-90) REVERT: C 527 GLU cc_start: 0.7051 (mt-10) cc_final: 0.6826 (pp20) REVERT: C 568 LYS cc_start: 0.7071 (mmtm) cc_final: 0.6861 (mttm) REVERT: D 15 SER cc_start: 0.7997 (t) cc_final: 0.7693 (p) REVERT: D 234 THR cc_start: 0.7241 (m) cc_final: 0.7028 (m) REVERT: D 275 GLU cc_start: 0.7946 (mt-10) cc_final: 0.7537 (mt-10) REVERT: E 210 ARG cc_start: 0.7770 (ttp80) cc_final: 0.7119 (ttt-90) REVERT: E 265 GLU cc_start: 0.6942 (mt-10) cc_final: 0.6738 (mt-10) REVERT: E 290 ASP cc_start: 0.7315 (t70) cc_final: 0.6937 (t0) REVERT: E 334 GLU cc_start: 0.8569 (mp0) cc_final: 0.8272 (mp0) REVERT: F 3 LEU cc_start: 0.6536 (mp) cc_final: 0.6213 (mp) REVERT: F 6 LYS cc_start: 0.7578 (tttt) cc_final: 0.6235 (ptpp) REVERT: F 13 TYR cc_start: 0.8991 (t80) cc_final: 0.8758 (t80) REVERT: F 223 LYS cc_start: 0.6999 (mttp) cc_final: 0.6250 (mppt) REVERT: F 280 ARG cc_start: 0.7419 (ttp-170) cc_final: 0.7207 (ttp-170) REVERT: F 318 ASP cc_start: 0.7522 (p0) cc_final: 0.6697 (t0) REVERT: F 363 ASN cc_start: 0.8093 (m-40) cc_final: 0.7565 (t0) REVERT: F 413 GLN cc_start: 0.7264 (mt0) cc_final: 0.7014 (mt0) REVERT: F 420 ARG cc_start: 0.6894 (mtm110) cc_final: 0.6635 (mtm-85) REVERT: G 15 ARG cc_start: 0.6606 (mtt180) cc_final: 0.6390 (mtp85) REVERT: G 17 GLN cc_start: 0.6945 (mm-40) cc_final: 0.6639 (mm110) REVERT: G 19 ARG cc_start: 0.6685 (ttm110) cc_final: 0.6349 (ttm110) REVERT: G 47 MET cc_start: 0.5410 (ppp) cc_final: 0.5189 (tpp) REVERT: G 148 LYS cc_start: 0.5872 (mtpt) cc_final: 0.5628 (mttm) REVERT: G 177 ARG cc_start: 0.6836 (ttm110) cc_final: 0.6211 (ttt-90) REVERT: G 187 GLU cc_start: 0.7110 (mm-30) cc_final: 0.6698 (mm-30) REVERT: H 1 MET cc_start: 0.3170 (mpp) cc_final: 0.2799 (mtm) REVERT: J 81 GLU cc_start: 0.5453 (pp20) cc_final: 0.4820 (tt0) REVERT: J 88 ARG cc_start: 0.5285 (ptm160) cc_final: 0.4622 (ttp-170) REVERT: J 89 GLU cc_start: 0.5176 (tp30) cc_final: 0.4890 (mm-30) REVERT: J 115 LEU cc_start: 0.5101 (tt) cc_final: 0.4869 (tp) REVERT: K 104 MET cc_start: 0.6393 (mtp) cc_final: 0.5851 (tpt) REVERT: L 81 GLU cc_start: 0.6912 (tt0) cc_final: 0.6449 (mt-10) REVERT: L 110 GLU cc_start: 0.7186 (mt-10) cc_final: 0.6808 (tt0) REVERT: L 142 LEU cc_start: 0.6559 (pt) cc_final: 0.5913 (mt) REVERT: L 160 LYS cc_start: 0.6321 (mmtp) cc_final: 0.5659 (mmpt) REVERT: L 168 LEU cc_start: 0.6808 (pp) cc_final: 0.6429 (tt) REVERT: L 172 ASP cc_start: 0.7550 (t70) cc_final: 0.7112 (m-30) outliers start: 0 outliers final: 0 residues processed: 545 average time/residue: 0.2236 time to fit residues: 182.5882 Evaluate side-chains 342 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 342 time to evaluate : 1.080 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 197 optimal weight: 8.9990 chunk 215 optimal weight: 0.9980 chunk 20 optimal weight: 6.9990 chunk 132 optimal weight: 9.9990 chunk 261 optimal weight: 7.9990 chunk 248 optimal weight: 10.0000 chunk 207 optimal weight: 0.9990 chunk 155 optimal weight: 1.9990 chunk 244 optimal weight: 9.9990 chunk 183 optimal weight: 5.9990 chunk 298 optimal weight: 4.9990 overall best weight: 2.9988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 290 ASN B 397 GLN D 363 ASN D 364 ASN D 437 GLN E 252 HIS E 338 GLN F 465 GLN G 68 GLN H 82 GLN J 124 ASN L 74 GLN Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.125648 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.101110 restraints weight = 43014.421| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 1.35 r_work: 0.2971 rms_B_bonded: 2.09 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 30114 Z= 0.158 Angle : 0.552 8.428 40813 Z= 0.285 Chirality : 0.045 0.149 4572 Planarity : 0.005 0.062 5333 Dihedral : 6.408 117.927 4259 Min Nonbonded Distance : 2.008 Molprobity Statistics. All-atom Clashscore : 3.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 0.91 % Allowed : 6.42 % Favored : 92.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 1.00 (0.14), residues: 3764 helix: 1.52 (0.14), residues: 1582 sheet: 0.18 (0.22), residues: 607 loop : 0.11 (0.16), residues: 1575 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 146 TYR 0.020 0.001 TYR E 13 PHE 0.021 0.002 PHE A 230 TRP 0.011 0.001 TRP C 119 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00372 (30114) covalent geometry : angle 0.55212 (40813) hydrogen bonds : bond 0.05145 ( 1247) hydrogen bonds : angle 4.59066 ( 3558) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 340 time to evaluate : 1.087 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.6967 (mtm-85) cc_final: 0.6661 (mmt90) REVERT: A 456 GLU cc_start: 0.8483 (tt0) cc_final: 0.7975 (mt-10) REVERT: A 469 GLN cc_start: 0.7733 (mm-40) cc_final: 0.7418 (mt0) REVERT: A 481 ARG cc_start: 0.7590 (mmm-85) cc_final: 0.7373 (mtp85) REVERT: A 569 GLU cc_start: 0.6485 (tt0) cc_final: 0.6049 (mm-30) REVERT: B 124 LYS cc_start: 0.6618 (mmtm) cc_final: 0.6185 (mtpp) REVERT: B 197 ARG cc_start: 0.8107 (ttp-110) cc_final: 0.7794 (ttp-110) REVERT: B 460 ARG cc_start: 0.7910 (ttm-80) cc_final: 0.7651 (ttm170) REVERT: B 516 MET cc_start: 0.7862 (mtm) cc_final: 0.7423 (mtm) REVERT: B 520 LEU cc_start: 0.8429 (mm) cc_final: 0.8037 (mm) REVERT: B 524 LYS cc_start: 0.5984 (mtmt) cc_final: 0.5482 (tttm) REVERT: C 481 ARG cc_start: 0.7685 (mtp85) cc_final: 0.7395 (ttt-90) REVERT: E 210 ARG cc_start: 0.8327 (ttp80) cc_final: 0.7982 (ttt-90) REVERT: F 3 LEU cc_start: 0.7113 (mp) cc_final: 0.6836 (mp) REVERT: F 6 LYS cc_start: 0.7802 (tttt) cc_final: 0.7001 (ptpp) REVERT: F 13 TYR cc_start: 0.9135 (t80) cc_final: 0.8872 (t80) REVERT: F 318 ASP cc_start: 0.7878 (p0) cc_final: 0.7124 (t0) REVERT: G 15 ARG cc_start: 0.8205 (mtt180) cc_final: 0.7902 (mtp85) REVERT: G 47 MET cc_start: 0.6354 (ppp) cc_final: 0.6032 (ttp) REVERT: G 105 LYS cc_start: 0.5471 (tptt) cc_final: 0.4764 (tppt) REVERT: G 148 LYS cc_start: 0.7170 (mtpt) cc_final: 0.6895 (mttm) REVERT: G 177 ARG cc_start: 0.8121 (ttm110) cc_final: 0.7804 (ttt-90) REVERT: H 87 GLU cc_start: 0.6578 (mp0) cc_final: 0.6190 (mm-30) REVERT: J 81 GLU cc_start: 0.6756 (pp20) cc_final: 0.5977 (tt0) REVERT: J 88 ARG cc_start: 0.5802 (ptm160) cc_final: 0.5149 (tpt-90) REVERT: J 89 GLU cc_start: 0.5729 (tp30) cc_final: 0.5457 (mm-30) REVERT: K 104 MET cc_start: 0.6959 (mtp) cc_final: 0.6358 (tpt) REVERT: L 81 GLU cc_start: 0.7524 (tt0) cc_final: 0.7147 (mt-10) REVERT: L 105 ARG cc_start: 0.7387 (mtp85) cc_final: 0.6920 (mtt90) REVERT: L 110 GLU cc_start: 0.6957 (mt-10) cc_final: 0.6680 (tt0) REVERT: L 142 LEU cc_start: 0.6879 (pt) cc_final: 0.6455 (mt) REVERT: L 160 LYS cc_start: 0.7503 (mmtp) cc_final: 0.7071 (mmpt) REVERT: L 172 ASP cc_start: 0.7877 (t70) cc_final: 0.7631 (m-30) outliers start: 28 outliers final: 19 residues processed: 358 average time/residue: 0.2066 time to fit residues: 113.7640 Evaluate side-chains 313 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 294 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain L residue 68 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 49 optimal weight: 8.9990 chunk 118 optimal weight: 5.9990 chunk 270 optimal weight: 9.9990 chunk 137 optimal weight: 9.9990 chunk 307 optimal weight: 6.9990 chunk 42 optimal weight: 8.9990 chunk 95 optimal weight: 6.9990 chunk 169 optimal weight: 9.9990 chunk 251 optimal weight: 5.9990 chunk 170 optimal weight: 5.9990 chunk 138 optimal weight: 7.9990 overall best weight: 6.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 418 HIS C 496 GLN D 170 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 148 GLN F 23 ASN F 323 HIS F 425 GLN L 74 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3450 r_free = 0.3450 target = 0.122714 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.098182 restraints weight = 43408.612| |-----------------------------------------------------------------------------| r_work (start): 0.3094 rms_B_bonded: 1.56 r_work: 0.2909 rms_B_bonded: 2.14 restraints_weight: 0.5000 r_work: 0.2795 rms_B_bonded: 3.61 restraints_weight: 0.2500 r_work (final): 0.2795 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.063 30114 Z= 0.281 Angle : 0.672 8.841 40813 Z= 0.348 Chirality : 0.050 0.187 4572 Planarity : 0.006 0.065 5333 Dihedral : 6.912 106.696 4259 Min Nonbonded Distance : 1.807 Molprobity Statistics. All-atom Clashscore : 4.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 1.91 % Allowed : 9.41 % Favored : 88.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.34 (0.14), residues: 3764 helix: 1.00 (0.13), residues: 1577 sheet: -0.11 (0.22), residues: 592 loop : -0.31 (0.15), residues: 1595 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG E 146 TYR 0.016 0.002 TYR E 13 PHE 0.034 0.002 PHE A 230 TRP 0.038 0.002 TRP J 100 HIS 0.008 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00698 (30114) covalent geometry : angle 0.67155 (40813) hydrogen bonds : bond 0.06314 ( 1247) hydrogen bonds : angle 4.76429 ( 3558) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 59 poor density : 295 time to evaluate : 1.082 Fit side-chains REVERT: A 329 ARG cc_start: 0.7362 (mtm-85) cc_final: 0.6848 (mmt90) REVERT: A 456 GLU cc_start: 0.8442 (tt0) cc_final: 0.7867 (mt-10) REVERT: A 469 GLN cc_start: 0.7579 (mm-40) cc_final: 0.7282 (mt0) REVERT: A 541 GLN cc_start: 0.6988 (OUTLIER) cc_final: 0.6629 (mt0) REVERT: A 569 GLU cc_start: 0.6697 (tt0) cc_final: 0.6055 (mm-30) REVERT: B 460 ARG cc_start: 0.7980 (ttm-80) cc_final: 0.7729 (ttm170) REVERT: B 509 MET cc_start: 0.7477 (mmt) cc_final: 0.7053 (mmt) REVERT: B 520 LEU cc_start: 0.8393 (mm) cc_final: 0.7874 (mm) REVERT: B 524 LYS cc_start: 0.6150 (mtmt) cc_final: 0.5659 (tttm) REVERT: C 154 ARG cc_start: 0.8560 (mtp85) cc_final: 0.8077 (mtm180) REVERT: C 480 GLU cc_start: 0.7728 (mm-30) cc_final: 0.7191 (mm-30) REVERT: C 481 ARG cc_start: 0.7735 (mtp85) cc_final: 0.7357 (ttt-90) REVERT: D 61 GLU cc_start: 0.7271 (OUTLIER) cc_final: 0.6872 (mp0) REVERT: D 182 GLU cc_start: 0.6544 (tm-30) cc_final: 0.6127 (mm-30) REVERT: E 210 ARG cc_start: 0.8270 (ttp80) cc_final: 0.8011 (ttt-90) REVERT: E 334 GLU cc_start: 0.8590 (OUTLIER) cc_final: 0.8342 (mt-10) REVERT: F 3 LEU cc_start: 0.7176 (mp) cc_final: 0.6921 (mp) REVERT: F 6 LYS cc_start: 0.8034 (tttt) cc_final: 0.7137 (mttp) REVERT: F 68 LEU cc_start: 0.9129 (OUTLIER) cc_final: 0.8738 (mp) REVERT: F 318 ASP cc_start: 0.7917 (p0) cc_final: 0.7255 (t0) REVERT: G 47 MET cc_start: 0.6439 (ppp) cc_final: 0.5929 (ttp) REVERT: G 177 ARG cc_start: 0.8332 (ttm110) cc_final: 0.8110 (ttm-80) REVERT: H 68 LEU cc_start: 0.4001 (OUTLIER) cc_final: 0.3777 (tp) REVERT: J 81 GLU cc_start: 0.6721 (pp20) cc_final: 0.5900 (tt0) REVERT: J 88 ARG cc_start: 0.5641 (ptm160) cc_final: 0.5183 (tmm-80) REVERT: J 99 GLU cc_start: 0.5924 (mm-30) cc_final: 0.5675 (mp0) REVERT: K 104 MET cc_start: 0.6925 (mtp) cc_final: 0.6284 (tpt) REVERT: L 110 GLU cc_start: 0.7055 (mt-10) cc_final: 0.6772 (tt0) REVERT: L 142 LEU cc_start: 0.6557 (pt) cc_final: 0.5934 (mt) REVERT: L 160 LYS cc_start: 0.7667 (mmtp) cc_final: 0.7077 (mmpt) REVERT: L 172 ASP cc_start: 0.8011 (t70) cc_final: 0.7735 (m-30) outliers start: 59 outliers final: 37 residues processed: 332 average time/residue: 0.1867 time to fit residues: 97.8512 Evaluate side-chains 310 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 268 time to evaluate : 0.970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 541 GLN Chi-restraints excluded: chain B residue 36 VAL Chi-restraints excluded: chain B residue 45 ASP Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 68 LEU Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 158 THR Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 68 LEU Chi-restraints excluded: chain I residue 81 THR Chi-restraints excluded: chain L residue 68 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 260 optimal weight: 10.0000 chunk 206 optimal weight: 8.9990 chunk 155 optimal weight: 0.9990 chunk 10 optimal weight: 0.9990 chunk 293 optimal weight: 3.9990 chunk 31 optimal weight: 6.9990 chunk 311 optimal weight: 4.9990 chunk 86 optimal weight: 0.9980 chunk 118 optimal weight: 1.9990 chunk 342 optimal weight: 9.9990 chunk 239 optimal weight: 0.3980 overall best weight: 1.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN C 238 GLN C 316 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.127082 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3156 r_free = 0.3156 target = 0.102299 restraints weight = 42727.156| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 1.54 r_work: 0.2988 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2869 rms_B_bonded: 3.84 restraints_weight: 0.2500 r_work (final): 0.2869 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 30114 Z= 0.101 Angle : 0.485 8.876 40813 Z= 0.249 Chirality : 0.042 0.154 4572 Planarity : 0.004 0.052 5333 Dihedral : 6.359 95.243 4259 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 3.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.54 % Favored : 98.46 % Rotamer: Outliers : 1.14 % Allowed : 11.22 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.79 (0.14), residues: 3764 helix: 1.45 (0.14), residues: 1588 sheet: 0.04 (0.22), residues: 591 loop : -0.13 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG G 146 TYR 0.022 0.001 TYR E 13 PHE 0.014 0.001 PHE C 230 TRP 0.019 0.001 TRP J 100 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00214 (30114) covalent geometry : angle 0.48474 (40813) hydrogen bonds : bond 0.04094 ( 1247) hydrogen bonds : angle 4.29936 ( 3558) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 298 time to evaluate : 1.063 Fit side-chains REVERT: A 134 VAL cc_start: 0.9070 (OUTLIER) cc_final: 0.8688 (t) REVERT: A 329 ARG cc_start: 0.7214 (mtm-85) cc_final: 0.6781 (mmp80) REVERT: A 456 GLU cc_start: 0.8483 (tt0) cc_final: 0.7927 (mt-10) REVERT: A 469 GLN cc_start: 0.7625 (mm-40) cc_final: 0.7333 (mt0) REVERT: A 481 ARG cc_start: 0.7576 (mmm-85) cc_final: 0.7298 (mtp85) REVERT: A 569 GLU cc_start: 0.6564 (tt0) cc_final: 0.5962 (mm-30) REVERT: B 408 ARG cc_start: 0.7915 (ttm-80) cc_final: 0.7666 (ttt180) REVERT: B 509 MET cc_start: 0.7333 (mmt) cc_final: 0.7085 (mmt) REVERT: B 516 MET cc_start: 0.7853 (mtm) cc_final: 0.7274 (mtm) REVERT: B 520 LEU cc_start: 0.8343 (mm) cc_final: 0.7948 (mm) REVERT: B 524 LYS cc_start: 0.6169 (mtmt) cc_final: 0.5656 (tttm) REVERT: C 481 ARG cc_start: 0.7714 (mtp85) cc_final: 0.7342 (ttt-90) REVERT: D 206 GLN cc_start: 0.8141 (mm-40) cc_final: 0.7849 (pp30) REVERT: E 210 ARG cc_start: 0.8239 (ttp80) cc_final: 0.7954 (ttt-90) REVERT: F 6 LYS cc_start: 0.7884 (tttt) cc_final: 0.7153 (ptpp) REVERT: F 182 GLU cc_start: 0.6243 (OUTLIER) cc_final: 0.6009 (mp0) REVERT: F 318 ASP cc_start: 0.7841 (p0) cc_final: 0.7263 (t0) REVERT: G 15 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7917 (mtp85) REVERT: G 47 MET cc_start: 0.6460 (ppp) cc_final: 0.6057 (ttp) REVERT: G 187 GLU cc_start: 0.8205 (mm-30) cc_final: 0.7994 (mm-30) REVERT: J 81 GLU cc_start: 0.6675 (pp20) cc_final: 0.5979 (tt0) REVERT: J 88 ARG cc_start: 0.5662 (ptm160) cc_final: 0.5196 (tmm-80) REVERT: K 104 MET cc_start: 0.6725 (mtp) cc_final: 0.6123 (tpt) REVERT: L 110 GLU cc_start: 0.6964 (mt-10) cc_final: 0.6721 (tt0) REVERT: L 142 LEU cc_start: 0.6470 (pt) cc_final: 0.5911 (mt) REVERT: L 160 LYS cc_start: 0.7471 (mmtp) cc_final: 0.6900 (mmpt) REVERT: L 172 ASP cc_start: 0.8071 (t70) cc_final: 0.7738 (m-30) outliers start: 35 outliers final: 20 residues processed: 318 average time/residue: 0.1911 time to fit residues: 95.2951 Evaluate side-chains 307 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 285 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 474 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 1 MET Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 44 optimal weight: 7.9990 chunk 189 optimal weight: 10.0000 chunk 114 optimal weight: 10.0000 chunk 178 optimal weight: 7.9990 chunk 211 optimal weight: 8.9990 chunk 348 optimal weight: 0.0060 chunk 37 optimal weight: 10.0000 chunk 125 optimal weight: 9.9990 chunk 115 optimal weight: 8.9990 chunk 273 optimal weight: 4.9990 chunk 54 optimal weight: 5.9990 overall best weight: 5.4004 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 437 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.123344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.098537 restraints weight = 43209.630| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 1.53 r_work: 0.2929 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8567 moved from start: 0.2289 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.058 30114 Z= 0.233 Angle : 0.612 7.852 40813 Z= 0.315 Chirality : 0.047 0.161 4572 Planarity : 0.006 0.053 5333 Dihedral : 6.420 90.451 4259 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Rotamer: Outliers : 2.37 % Allowed : 11.64 % Favored : 85.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.40 (0.14), residues: 3764 helix: 1.17 (0.13), residues: 1577 sheet: -0.12 (0.22), residues: 593 loop : -0.40 (0.15), residues: 1594 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 401 TYR 0.019 0.002 TYR E 13 PHE 0.033 0.002 PHE A 230 TRP 0.021 0.002 TRP J 100 HIS 0.007 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00578 (30114) covalent geometry : angle 0.61205 (40813) hydrogen bonds : bond 0.05613 ( 1247) hydrogen bonds : angle 4.55678 ( 3558) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 73 poor density : 282 time to evaluate : 0.954 Fit side-chains REVERT: A 134 VAL cc_start: 0.9109 (OUTLIER) cc_final: 0.8703 (t) REVERT: A 180 GLU cc_start: 0.8253 (OUTLIER) cc_final: 0.7940 (pm20) REVERT: A 329 ARG cc_start: 0.7387 (mtm-85) cc_final: 0.6909 (mmp80) REVERT: A 456 GLU cc_start: 0.8442 (tt0) cc_final: 0.7881 (mt-10) REVERT: A 469 GLN cc_start: 0.7614 (mm-40) cc_final: 0.7306 (mt0) REVERT: A 481 ARG cc_start: 0.7652 (mmm-85) cc_final: 0.7388 (mtp85) REVERT: A 569 GLU cc_start: 0.6704 (tt0) cc_final: 0.6021 (mm-30) REVERT: B 211 ILE cc_start: 0.8136 (OUTLIER) cc_final: 0.7560 (tp) REVERT: B 520 LEU cc_start: 0.8430 (mm) cc_final: 0.7953 (mm) REVERT: B 524 LYS cc_start: 0.6237 (mtmt) cc_final: 0.5708 (tttm) REVERT: C 480 GLU cc_start: 0.7778 (mm-30) cc_final: 0.7211 (mm-30) REVERT: C 481 ARG cc_start: 0.7743 (mtp85) cc_final: 0.7351 (ttt-90) REVERT: E 210 ARG cc_start: 0.8329 (ttp80) cc_final: 0.8097 (ttt-90) REVERT: E 334 GLU cc_start: 0.8499 (OUTLIER) cc_final: 0.8222 (mt-10) REVERT: F 3 LEU cc_start: 0.7151 (mp) cc_final: 0.6929 (mp) REVERT: F 6 LYS cc_start: 0.8027 (tttt) cc_final: 0.7138 (mttp) REVERT: F 182 GLU cc_start: 0.6278 (OUTLIER) cc_final: 0.5528 (mt-10) REVERT: F 318 ASP cc_start: 0.7941 (p0) cc_final: 0.7369 (t0) REVERT: G 47 MET cc_start: 0.6414 (ppp) cc_final: 0.5947 (ttp) REVERT: H 87 GLU cc_start: 0.6577 (mp0) cc_final: 0.6326 (mp0) REVERT: J 88 ARG cc_start: 0.5380 (ptm160) cc_final: 0.4791 (tmm160) REVERT: J 99 GLU cc_start: 0.5852 (mm-30) cc_final: 0.5574 (mp0) REVERT: J 109 LEU cc_start: 0.5867 (OUTLIER) cc_final: 0.5627 (tp) REVERT: K 104 MET cc_start: 0.6984 (mtp) cc_final: 0.6364 (tpt) REVERT: L 110 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6778 (tt0) REVERT: L 155 VAL cc_start: 0.7336 (OUTLIER) cc_final: 0.6885 (t) REVERT: L 160 LYS cc_start: 0.7667 (mmtp) cc_final: 0.7061 (mmpt) REVERT: L 172 ASP cc_start: 0.8070 (t70) cc_final: 0.7802 (m-30) outliers start: 73 outliers final: 51 residues processed: 330 average time/residue: 0.1841 time to fit residues: 96.6761 Evaluate side-chains 329 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 271 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 180 GLU Chi-restraints excluded: chain A residue 255 CYS Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 482 LEU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 96 ILE Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 155 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 158 optimal weight: 2.9990 chunk 76 optimal weight: 10.0000 chunk 61 optimal weight: 6.9990 chunk 64 optimal weight: 2.9990 chunk 253 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 296 optimal weight: 1.9990 chunk 242 optimal weight: 4.9990 chunk 240 optimal weight: 0.9990 chunk 257 optimal weight: 10.0000 chunk 361 optimal weight: 6.9990 overall best weight: 1.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN J 74 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.126549 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.101108 restraints weight = 43202.840| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 1.35 r_work: 0.2973 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.2858 rms_B_bonded: 3.73 restraints_weight: 0.2500 r_work (final): 0.2858 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.036 30114 Z= 0.108 Angle : 0.492 8.596 40813 Z= 0.251 Chirality : 0.042 0.161 4572 Planarity : 0.004 0.056 5333 Dihedral : 6.056 88.586 4259 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 3.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.51 % Favored : 98.49 % Rotamer: Outliers : 1.69 % Allowed : 12.97 % Favored : 85.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3764 helix: 1.45 (0.14), residues: 1590 sheet: -0.01 (0.22), residues: 589 loop : -0.23 (0.15), residues: 1585 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.021 0.001 TYR E 13 PHE 0.014 0.001 PHE C 230 TRP 0.022 0.001 TRP J 100 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00240 (30114) covalent geometry : angle 0.49218 (40813) hydrogen bonds : bond 0.04164 ( 1247) hydrogen bonds : angle 4.28184 ( 3558) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 300 time to evaluate : 1.030 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7289 (mtm-85) cc_final: 0.6926 (mmp80) REVERT: A 456 GLU cc_start: 0.8383 (tt0) cc_final: 0.7892 (mt-10) REVERT: A 469 GLN cc_start: 0.7617 (mm-40) cc_final: 0.7341 (mt0) REVERT: A 481 ARG cc_start: 0.7597 (mmm-85) cc_final: 0.7380 (mtp85) REVERT: A 569 GLU cc_start: 0.6608 (tt0) cc_final: 0.5944 (mm-30) REVERT: B 211 ILE cc_start: 0.7998 (OUTLIER) cc_final: 0.7596 (tp) REVERT: B 509 MET cc_start: 0.7212 (mmt) cc_final: 0.6906 (mmm) REVERT: B 516 MET cc_start: 0.7884 (mtm) cc_final: 0.7319 (mtm) REVERT: B 520 LEU cc_start: 0.8461 (mm) cc_final: 0.8157 (mm) REVERT: B 524 LYS cc_start: 0.6251 (mtmt) cc_final: 0.5738 (tttm) REVERT: C 481 ARG cc_start: 0.7740 (mtp85) cc_final: 0.7336 (ttt-90) REVERT: D 265 GLU cc_start: 0.8115 (mm-30) cc_final: 0.7914 (mp0) REVERT: E 210 ARG cc_start: 0.8307 (ttp80) cc_final: 0.7997 (ttt-90) REVERT: E 334 GLU cc_start: 0.8421 (OUTLIER) cc_final: 0.8178 (mt-10) REVERT: F 6 LYS cc_start: 0.7888 (tttt) cc_final: 0.7036 (mttp) REVERT: F 182 GLU cc_start: 0.6289 (OUTLIER) cc_final: 0.5548 (mt-10) REVERT: F 318 ASP cc_start: 0.7794 (p0) cc_final: 0.7265 (t0) REVERT: G 15 ARG cc_start: 0.8248 (mtt180) cc_final: 0.7911 (mtp85) REVERT: G 47 MET cc_start: 0.6496 (ppp) cc_final: 0.6072 (ttp) REVERT: G 64 LEU cc_start: 0.5262 (OUTLIER) cc_final: 0.4539 (pp) REVERT: G 187 GLU cc_start: 0.8251 (mm-30) cc_final: 0.8043 (mm-30) REVERT: H 87 GLU cc_start: 0.6644 (mp0) cc_final: 0.6442 (mp0) REVERT: J 88 ARG cc_start: 0.5362 (ptm160) cc_final: 0.4792 (tmm160) REVERT: J 105 ARG cc_start: 0.7264 (ttm170) cc_final: 0.6986 (ttm-80) REVERT: K 104 MET cc_start: 0.6776 (mtp) cc_final: 0.6274 (tpt) REVERT: L 110 GLU cc_start: 0.6944 (mt-10) cc_final: 0.6742 (tt0) REVERT: L 142 LEU cc_start: 0.6753 (pp) cc_final: 0.6017 (mt) REVERT: L 160 LYS cc_start: 0.7508 (mmtp) cc_final: 0.6905 (mmpt) REVERT: L 172 ASP cc_start: 0.8011 (t70) cc_final: 0.7796 (m-30) outliers start: 52 outliers final: 36 residues processed: 333 average time/residue: 0.1936 time to fit residues: 100.9467 Evaluate side-chains 328 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 288 time to evaluate : 1.033 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 263 THR Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 303 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 87 optimal weight: 8.9990 chunk 2 optimal weight: 9.9990 chunk 99 optimal weight: 9.9990 chunk 223 optimal weight: 0.8980 chunk 272 optimal weight: 9.9990 chunk 208 optimal weight: 9.9990 chunk 371 optimal weight: 20.0000 chunk 324 optimal weight: 20.0000 chunk 313 optimal weight: 9.9990 overall best weight: 7.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 437 GLN E 148 GLN H 82 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3444 r_free = 0.3444 target = 0.122367 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.097731 restraints weight = 43024.071| |-----------------------------------------------------------------------------| r_work (start): 0.3100 rms_B_bonded: 1.32 r_work: 0.2927 rms_B_bonded: 2.02 restraints_weight: 0.5000 r_work: 0.2823 rms_B_bonded: 3.36 restraints_weight: 0.2500 r_work (final): 0.2823 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 30114 Z= 0.298 Angle : 0.664 8.447 40813 Z= 0.342 Chirality : 0.049 0.168 4572 Planarity : 0.006 0.063 5333 Dihedral : 6.450 84.981 4259 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.92 % Favored : 97.08 % Rotamer: Outliers : 2.69 % Allowed : 13.10 % Favored : 84.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.21 (0.14), residues: 3764 helix: 1.01 (0.13), residues: 1568 sheet: -0.22 (0.22), residues: 590 loop : -0.50 (0.15), residues: 1606 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 196 TYR 0.017 0.002 TYR E 13 PHE 0.036 0.003 PHE A 230 TRP 0.021 0.002 TRP J 100 HIS 0.007 0.002 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00738 (30114) covalent geometry : angle 0.66439 (40813) hydrogen bonds : bond 0.06062 ( 1247) hydrogen bonds : angle 4.65094 ( 3558) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 358 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 83 poor density : 275 time to evaluate : 1.121 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7402 (mtm-85) cc_final: 0.6977 (mmp80) REVERT: A 456 GLU cc_start: 0.8327 (tt0) cc_final: 0.7826 (mt-10) REVERT: A 481 ARG cc_start: 0.7657 (mmm-85) cc_final: 0.7411 (mtp85) REVERT: A 569 GLU cc_start: 0.6767 (tt0) cc_final: 0.5979 (mm-30) REVERT: B 211 ILE cc_start: 0.8150 (OUTLIER) cc_final: 0.7553 (tp) REVERT: B 323 MET cc_start: 0.8667 (OUTLIER) cc_final: 0.8120 (mtp) REVERT: B 509 MET cc_start: 0.7490 (mmt) cc_final: 0.7192 (mmm) REVERT: B 520 LEU cc_start: 0.8453 (OUTLIER) cc_final: 0.8148 (tp) REVERT: B 524 LYS cc_start: 0.6281 (mtmt) cc_final: 0.5716 (tttm) REVERT: C 480 GLU cc_start: 0.7738 (mm-30) cc_final: 0.7173 (mm-30) REVERT: C 481 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7272 (ttt-90) REVERT: D 61 GLU cc_start: 0.7307 (OUTLIER) cc_final: 0.6907 (mp0) REVERT: D 265 GLU cc_start: 0.8063 (mm-30) cc_final: 0.7832 (mp0) REVERT: E 210 ARG cc_start: 0.8287 (ttp80) cc_final: 0.8054 (ttt-90) REVERT: E 334 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.8181 (mt-10) REVERT: F 6 LYS cc_start: 0.8010 (tttt) cc_final: 0.7090 (mttp) REVERT: F 182 GLU cc_start: 0.6460 (OUTLIER) cc_final: 0.5669 (mt-10) REVERT: F 318 ASP cc_start: 0.7942 (p0) cc_final: 0.7380 (t0) REVERT: G 47 MET cc_start: 0.6394 (ppp) cc_final: 0.5931 (ttp) REVERT: G 123 THR cc_start: 0.5497 (OUTLIER) cc_final: 0.5194 (m) REVERT: H 87 GLU cc_start: 0.6769 (mp0) cc_final: 0.6489 (mp0) REVERT: J 88 ARG cc_start: 0.5370 (ptm160) cc_final: 0.4903 (tmm-80) REVERT: J 99 GLU cc_start: 0.5855 (mm-30) cc_final: 0.5597 (mp0) REVERT: J 105 ARG cc_start: 0.7261 (ttm170) cc_final: 0.6991 (ttm-80) REVERT: J 109 LEU cc_start: 0.5697 (OUTLIER) cc_final: 0.5359 (tp) REVERT: K 104 MET cc_start: 0.6991 (mtp) cc_final: 0.6377 (tpt) REVERT: L 110 GLU cc_start: 0.7044 (mt-10) cc_final: 0.6816 (tt0) REVERT: L 160 LYS cc_start: 0.7631 (mmtp) cc_final: 0.7061 (mmpt) REVERT: L 172 ASP cc_start: 0.7988 (t70) cc_final: 0.7727 (m-30) outliers start: 83 outliers final: 61 residues processed: 330 average time/residue: 0.1944 time to fit residues: 101.3733 Evaluate side-chains 334 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 265 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 486 VAL Chi-restraints excluded: chain A residue 570 ILE Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 338 SER Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 61 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 9 THR Chi-restraints excluded: chain E residue 12 THR Chi-restraints excluded: chain E residue 26 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 137 THR Chi-restraints excluded: chain E residue 211 THR Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 3 LEU Chi-restraints excluded: chain F residue 9 THR Chi-restraints excluded: chain F residue 79 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 396 VAL Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain H residue 90 MET Chi-restraints excluded: chain H residue 102 ILE Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain J residue 109 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 316 optimal weight: 20.0000 chunk 44 optimal weight: 3.9990 chunk 327 optimal weight: 1.9990 chunk 310 optimal weight: 1.9990 chunk 140 optimal weight: 0.9990 chunk 176 optimal weight: 1.9990 chunk 330 optimal weight: 7.9990 chunk 36 optimal weight: 5.9990 chunk 199 optimal weight: 0.9990 chunk 224 optimal weight: 1.9990 chunk 347 optimal weight: 8.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN B 246 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN E 142 ASN E 148 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3487 r_free = 0.3487 target = 0.125497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3140 r_free = 0.3140 target = 0.100819 restraints weight = 43022.499| |-----------------------------------------------------------------------------| r_work (start): 0.3143 rms_B_bonded: 1.35 r_work: 0.2976 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.2466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 30114 Z= 0.111 Angle : 0.501 8.191 40813 Z= 0.257 Chirality : 0.042 0.163 4572 Planarity : 0.004 0.060 5333 Dihedral : 6.112 86.365 4259 Min Nonbonded Distance : 1.951 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer: Outliers : 2.04 % Allowed : 13.85 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.59 (0.14), residues: 3764 helix: 1.37 (0.14), residues: 1589 sheet: -0.05 (0.22), residues: 584 loop : -0.35 (0.15), residues: 1591 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.021 0.001 TYR E 13 PHE 0.016 0.001 PHE E 130 TRP 0.022 0.001 TRP J 100 HIS 0.004 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00250 (30114) covalent geometry : angle 0.50139 (40813) hydrogen bonds : bond 0.04304 ( 1247) hydrogen bonds : angle 4.32599 ( 3558) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 356 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 293 time to evaluate : 1.117 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7266 (mtm-85) cc_final: 0.6862 (mmp80) REVERT: A 456 GLU cc_start: 0.8416 (tt0) cc_final: 0.7899 (mt-10) REVERT: A 469 GLN cc_start: 0.7596 (mm110) cc_final: 0.7121 (mt0) REVERT: A 481 ARG cc_start: 0.7572 (mmm-85) cc_final: 0.7365 (mtp85) REVERT: A 565 GLU cc_start: 0.7481 (OUTLIER) cc_final: 0.7056 (mp0) REVERT: A 569 GLU cc_start: 0.6666 (tt0) cc_final: 0.5912 (mm-30) REVERT: B 211 ILE cc_start: 0.8003 (OUTLIER) cc_final: 0.7605 (tp) REVERT: B 323 MET cc_start: 0.8669 (OUTLIER) cc_final: 0.8104 (mtp) REVERT: B 509 MET cc_start: 0.7408 (mmt) cc_final: 0.7188 (mmm) REVERT: B 516 MET cc_start: 0.7883 (mtm) cc_final: 0.7319 (mtm) REVERT: B 520 LEU cc_start: 0.8462 (OUTLIER) cc_final: 0.8156 (mm) REVERT: B 524 LYS cc_start: 0.6177 (mtmt) cc_final: 0.5699 (tttm) REVERT: C 480 GLU cc_start: 0.7724 (mm-30) cc_final: 0.7174 (mm-30) REVERT: C 481 ARG cc_start: 0.7706 (mtp85) cc_final: 0.7260 (ttt-90) REVERT: D 265 GLU cc_start: 0.8083 (mm-30) cc_final: 0.7872 (mp0) REVERT: E 210 ARG cc_start: 0.8276 (ttp80) cc_final: 0.7966 (ttt-90) REVERT: E 334 GLU cc_start: 0.8366 (OUTLIER) cc_final: 0.8107 (mt-10) REVERT: F 6 LYS cc_start: 0.7943 (tttt) cc_final: 0.7099 (mttp) REVERT: F 182 GLU cc_start: 0.6423 (OUTLIER) cc_final: 0.5644 (mt-10) REVERT: F 318 ASP cc_start: 0.7871 (p0) cc_final: 0.7335 (t0) REVERT: G 15 ARG cc_start: 0.8245 (mtt180) cc_final: 0.7881 (mtp85) REVERT: G 47 MET cc_start: 0.6435 (ppp) cc_final: 0.6011 (ttp) REVERT: G 64 LEU cc_start: 0.5261 (OUTLIER) cc_final: 0.4505 (pp) REVERT: G 123 THR cc_start: 0.5373 (OUTLIER) cc_final: 0.5117 (m) REVERT: H 87 GLU cc_start: 0.6679 (mp0) cc_final: 0.6413 (mp0) REVERT: J 88 ARG cc_start: 0.5378 (ptm160) cc_final: 0.4869 (tmm-80) REVERT: J 99 GLU cc_start: 0.5803 (mm-30) cc_final: 0.5595 (mp0) REVERT: J 105 ARG cc_start: 0.7254 (ttm170) cc_final: 0.6936 (ttm-80) REVERT: K 104 MET cc_start: 0.6803 (mtp) cc_final: 0.6208 (tpt) REVERT: L 110 GLU cc_start: 0.6989 (mt-10) cc_final: 0.6776 (tt0) REVERT: L 141 GLU cc_start: 0.6356 (OUTLIER) cc_final: 0.5959 (tm-30) REVERT: L 142 LEU cc_start: 0.6859 (pp) cc_final: 0.5653 (mt) REVERT: L 160 LYS cc_start: 0.7376 (mmtp) cc_final: 0.6853 (mmpt) REVERT: L 161 THR cc_start: 0.8625 (p) cc_final: 0.8417 (m) REVERT: L 172 ASP cc_start: 0.7999 (t70) cc_final: 0.7769 (m-30) outliers start: 63 outliers final: 47 residues processed: 335 average time/residue: 0.1919 time to fit residues: 101.3891 Evaluate side-chains 338 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 56 poor density : 282 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 384 VAL Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 64 LEU Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 371 optimal weight: 8.9990 chunk 370 optimal weight: 5.9990 chunk 203 optimal weight: 0.6980 chunk 6 optimal weight: 7.9990 chunk 141 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 42 optimal weight: 9.9990 chunk 95 optimal weight: 4.9990 chunk 294 optimal weight: 1.9990 chunk 289 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 246 ASN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN F 170 GLN L 96 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3477 r_free = 0.3477 target = 0.124778 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3128 r_free = 0.3128 target = 0.099963 restraints weight = 42895.989| |-----------------------------------------------------------------------------| r_work (start): 0.3123 rms_B_bonded: 1.33 r_work: 0.2951 rms_B_bonded: 2.06 restraints_weight: 0.5000 r_work: 0.2842 rms_B_bonded: 3.47 restraints_weight: 0.2500 r_work (final): 0.2842 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8526 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 30114 Z= 0.156 Angle : 0.538 9.517 40813 Z= 0.275 Chirality : 0.044 0.166 4572 Planarity : 0.005 0.058 5333 Dihedral : 6.142 85.491 4259 Min Nonbonded Distance : 1.895 Molprobity Statistics. All-atom Clashscore : 4.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.26 % Favored : 97.74 % Rotamer: Outliers : 2.24 % Allowed : 13.72 % Favored : 84.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.60 (0.14), residues: 3764 helix: 1.40 (0.14), residues: 1579 sheet: -0.10 (0.22), residues: 587 loop : -0.34 (0.15), residues: 1598 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.018 0.001 TYR E 13 PHE 0.023 0.002 PHE A 230 TRP 0.021 0.001 TRP J 100 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00377 (30114) covalent geometry : angle 0.53827 (40813) hydrogen bonds : bond 0.04697 ( 1247) hydrogen bonds : angle 4.35606 ( 3558) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 345 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 276 time to evaluate : 1.090 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7331 (mtm-85) cc_final: 0.6912 (mmp80) REVERT: A 456 GLU cc_start: 0.8360 (tt0) cc_final: 0.7849 (mt-10) REVERT: A 481 ARG cc_start: 0.7612 (mmm-85) cc_final: 0.7410 (mtp85) REVERT: A 565 GLU cc_start: 0.7496 (OUTLIER) cc_final: 0.7051 (mp0) REVERT: A 569 GLU cc_start: 0.6757 (tt0) cc_final: 0.5963 (mm-30) REVERT: B 211 ILE cc_start: 0.8039 (OUTLIER) cc_final: 0.7582 (tp) REVERT: B 323 MET cc_start: 0.8671 (OUTLIER) cc_final: 0.8142 (mtp) REVERT: B 408 ARG cc_start: 0.8044 (tpt-90) cc_final: 0.7832 (ttt90) REVERT: B 520 LEU cc_start: 0.8470 (OUTLIER) cc_final: 0.8159 (mm) REVERT: B 524 LYS cc_start: 0.6296 (mtmt) cc_final: 0.5717 (tttm) REVERT: C 480 GLU cc_start: 0.7726 (mm-30) cc_final: 0.7156 (mm-30) REVERT: C 481 ARG cc_start: 0.7736 (mtp85) cc_final: 0.7315 (ttt-90) REVERT: D 206 GLN cc_start: 0.8359 (mm-40) cc_final: 0.8034 (pp30) REVERT: D 265 GLU cc_start: 0.8128 (mm-30) cc_final: 0.7920 (mp0) REVERT: E 210 ARG cc_start: 0.8273 (ttp80) cc_final: 0.7970 (ttt-90) REVERT: E 334 GLU cc_start: 0.8403 (OUTLIER) cc_final: 0.8182 (mt-10) REVERT: F 6 LYS cc_start: 0.7977 (tttt) cc_final: 0.7130 (mttp) REVERT: F 182 GLU cc_start: 0.6398 (OUTLIER) cc_final: 0.5602 (mt-10) REVERT: F 318 ASP cc_start: 0.7921 (p0) cc_final: 0.7403 (t0) REVERT: G 47 MET cc_start: 0.6442 (ppp) cc_final: 0.6035 (ttp) REVERT: G 123 THR cc_start: 0.5178 (OUTLIER) cc_final: 0.4904 (m) REVERT: H 87 GLU cc_start: 0.6699 (mp0) cc_final: 0.6435 (mp0) REVERT: J 88 ARG cc_start: 0.5343 (ptm160) cc_final: 0.4857 (tmm-80) REVERT: K 104 MET cc_start: 0.6896 (mtp) cc_final: 0.6198 (tpt) REVERT: L 110 GLU cc_start: 0.7019 (mt-10) cc_final: 0.6806 (tt0) REVERT: L 141 GLU cc_start: 0.6397 (OUTLIER) cc_final: 0.5963 (tm-30) REVERT: L 142 LEU cc_start: 0.6882 (pp) cc_final: 0.5635 (mt) REVERT: L 160 LYS cc_start: 0.7416 (mmtp) cc_final: 0.6905 (mmpt) REVERT: L 172 ASP cc_start: 0.8013 (t70) cc_final: 0.7781 (m-30) outliers start: 69 outliers final: 52 residues processed: 322 average time/residue: 0.1864 time to fit residues: 95.3917 Evaluate side-chains 330 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 270 time to evaluate : 1.023 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 241 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 544 VAL Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain E residue 470 ILE Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain L residue 68 VAL Chi-restraints excluded: chain L residue 80 LEU Chi-restraints excluded: chain L residue 141 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 295 optimal weight: 0.9980 chunk 339 optimal weight: 3.9990 chunk 288 optimal weight: 0.9990 chunk 147 optimal weight: 6.9990 chunk 325 optimal weight: 6.9990 chunk 258 optimal weight: 10.0000 chunk 284 optimal weight: 5.9990 chunk 272 optimal weight: 8.9990 chunk 286 optimal weight: 5.9990 chunk 250 optimal weight: 0.9980 chunk 219 optimal weight: 1.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3495 r_free = 0.3495 target = 0.126159 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3149 r_free = 0.3149 target = 0.101514 restraints weight = 42794.682| |-----------------------------------------------------------------------------| r_work (start): 0.3151 rms_B_bonded: 1.39 r_work: 0.2984 rms_B_bonded: 2.03 restraints_weight: 0.5000 r_work: 0.2875 rms_B_bonded: 3.44 restraints_weight: 0.2500 r_work (final): 0.2875 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8501 moved from start: 0.2534 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 30114 Z= 0.116 Angle : 0.501 9.829 40813 Z= 0.255 Chirality : 0.042 0.157 4572 Planarity : 0.004 0.062 5333 Dihedral : 5.994 86.035 4259 Min Nonbonded Distance : 1.958 Molprobity Statistics. All-atom Clashscore : 4.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.91 % Favored : 98.09 % Rotamer: Outliers : 1.88 % Allowed : 14.01 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.73 (0.14), residues: 3764 helix: 1.50 (0.14), residues: 1589 sheet: -0.04 (0.22), residues: 587 loop : -0.26 (0.15), residues: 1588 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG C 210 TYR 0.020 0.001 TYR E 13 PHE 0.014 0.001 PHE C 230 TRP 0.018 0.001 TRP J 100 HIS 0.005 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00270 (30114) covalent geometry : angle 0.50136 (40813) hydrogen bonds : bond 0.04133 ( 1247) hydrogen bonds : angle 4.23039 ( 3558) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 7528 Ramachandran restraints generated. 3764 Oldfield, 0 Emsley, 3764 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 282 time to evaluate : 1.205 Fit side-chains revert: symmetry clash REVERT: A 329 ARG cc_start: 0.7230 (mtm-85) cc_final: 0.6841 (mmp80) REVERT: A 456 GLU cc_start: 0.8324 (tt0) cc_final: 0.7821 (mt-10) REVERT: A 565 GLU cc_start: 0.7487 (OUTLIER) cc_final: 0.7052 (mp0) REVERT: A 569 GLU cc_start: 0.6716 (tt0) cc_final: 0.5940 (mm-30) REVERT: B 211 ILE cc_start: 0.8010 (OUTLIER) cc_final: 0.7645 (tp) REVERT: B 323 MET cc_start: 0.8649 (OUTLIER) cc_final: 0.8102 (mtp) REVERT: B 408 ARG cc_start: 0.8026 (tpt-90) cc_final: 0.7798 (ttt90) REVERT: B 520 LEU cc_start: 0.8478 (OUTLIER) cc_final: 0.8210 (mm) REVERT: B 524 LYS cc_start: 0.6240 (mtmt) cc_final: 0.5721 (tttm) REVERT: C 480 GLU cc_start: 0.7717 (mm-30) cc_final: 0.7148 (mm-30) REVERT: C 481 ARG cc_start: 0.7708 (mtp85) cc_final: 0.7290 (ttt-90) REVERT: D 206 GLN cc_start: 0.8323 (mm-40) cc_final: 0.7995 (pp30) REVERT: E 210 ARG cc_start: 0.8260 (ttp80) cc_final: 0.7940 (ttt-90) REVERT: E 334 GLU cc_start: 0.8392 (OUTLIER) cc_final: 0.8155 (mt-10) REVERT: F 6 LYS cc_start: 0.7930 (tttt) cc_final: 0.7114 (mttp) REVERT: F 182 GLU cc_start: 0.6414 (OUTLIER) cc_final: 0.5614 (mt-10) REVERT: F 318 ASP cc_start: 0.7823 (p0) cc_final: 0.7305 (t0) REVERT: G 47 MET cc_start: 0.6389 (ppp) cc_final: 0.6038 (ttp) REVERT: G 123 THR cc_start: 0.5146 (OUTLIER) cc_final: 0.4877 (m) REVERT: H 87 GLU cc_start: 0.6654 (mp0) cc_final: 0.6391 (mp0) REVERT: J 88 ARG cc_start: 0.5392 (ptm160) cc_final: 0.4888 (tmm-80) REVERT: K 104 MET cc_start: 0.6757 (mtp) cc_final: 0.6281 (tpt) REVERT: L 141 GLU cc_start: 0.6329 (tt0) cc_final: 0.5913 (tm-30) REVERT: L 142 LEU cc_start: 0.6680 (pp) cc_final: 0.5482 (mt) REVERT: L 160 LYS cc_start: 0.7387 (mmtp) cc_final: 0.6910 (mmpt) REVERT: L 172 ASP cc_start: 0.7954 (t70) cc_final: 0.7749 (m-30) outliers start: 58 outliers final: 48 residues processed: 321 average time/residue: 0.1961 time to fit residues: 99.4457 Evaluate side-chains 329 residues out of total 3083 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 55 poor density : 274 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 5 VAL Chi-restraints excluded: chain A residue 14 VAL Chi-restraints excluded: chain A residue 79 MET Chi-restraints excluded: chain A residue 134 VAL Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 296 VAL Chi-restraints excluded: chain A residue 327 THR Chi-restraints excluded: chain A residue 393 GLU Chi-restraints excluded: chain A residue 565 GLU Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 107 VAL Chi-restraints excluded: chain B residue 124 LYS Chi-restraints excluded: chain B residue 149 VAL Chi-restraints excluded: chain B residue 211 ILE Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 255 CYS Chi-restraints excluded: chain B residue 323 MET Chi-restraints excluded: chain B residue 410 ASP Chi-restraints excluded: chain B residue 520 LEU Chi-restraints excluded: chain B residue 544 VAL Chi-restraints excluded: chain C residue 3 GLN Chi-restraints excluded: chain C residue 138 VAL Chi-restraints excluded: chain C residue 235 SER Chi-restraints excluded: chain C residue 393 GLU Chi-restraints excluded: chain C residue 461 GLU Chi-restraints excluded: chain C residue 539 ILE Chi-restraints excluded: chain C residue 555 SER Chi-restraints excluded: chain C residue 558 GLU Chi-restraints excluded: chain D residue 79 VAL Chi-restraints excluded: chain D residue 135 ILE Chi-restraints excluded: chain D residue 228 THR Chi-restraints excluded: chain D residue 274 ARG Chi-restraints excluded: chain D residue 300 VAL Chi-restraints excluded: chain D residue 322 THR Chi-restraints excluded: chain D residue 353 ASP Chi-restraints excluded: chain E residue 39 THR Chi-restraints excluded: chain E residue 70 THR Chi-restraints excluded: chain E residue 79 VAL Chi-restraints excluded: chain E residue 88 MET Chi-restraints excluded: chain E residue 318 ASP Chi-restraints excluded: chain E residue 334 GLU Chi-restraints excluded: chain E residue 396 VAL Chi-restraints excluded: chain F residue 96 ILE Chi-restraints excluded: chain F residue 182 GLU Chi-restraints excluded: chain F residue 399 ILE Chi-restraints excluded: chain G residue 4 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 107 THR Chi-restraints excluded: chain G residue 123 THR Chi-restraints excluded: chain G residue 164 LEU Chi-restraints excluded: chain G residue 190 ASP Chi-restraints excluded: chain G residue 194 LEU Chi-restraints excluded: chain H residue 70 VAL Chi-restraints excluded: chain I residue 107 LEU Chi-restraints excluded: chain L residue 68 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 373 random chunks: chunk 31 optimal weight: 9.9990 chunk 361 optimal weight: 20.0000 chunk 57 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 367 optimal weight: 10.0000 chunk 210 optimal weight: 0.6980 chunk 254 optimal weight: 1.9990 chunk 181 optimal weight: 4.9990 chunk 226 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 overall best weight: 3.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 316 GLN ** D 323 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 363 ASN D 437 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.124541 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3117 r_free = 0.3117 target = 0.099242 restraints weight = 42864.015| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 1.38 r_work: 0.2938 rms_B_bonded: 2.12 restraints_weight: 0.5000 r_work: 0.2826 rms_B_bonded: 3.62 restraints_weight: 0.2500 r_work (final): 0.2826 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2589 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 30114 Z= 0.183 Angle : 0.560 10.417 40813 Z= 0.286 Chirality : 0.045 0.156 4572 Planarity : 0.005 0.059 5333 Dihedral : 6.141 83.655 4259 Min Nonbonded Distance : 1.884 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.39 % Favored : 97.61 % Rotamer: Outliers : 2.11 % Allowed : 13.92 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.80 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.56 (0.14), residues: 3764 helix: 1.37 (0.13), residues: 1579 sheet: -0.13 (0.22), residues: 589 loop : -0.35 (0.15), residues: 1596 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG F 420 TYR 0.018 0.002 TYR E 13 PHE 0.026 0.002 PHE A 230 TRP 0.017 0.001 TRP J 100 HIS 0.006 0.001 HIS A 185 Details of bonding type rmsd covalent geometry : bond 0.00449 (30114) covalent geometry : angle 0.56011 (40813) hydrogen bonds : bond 0.04894 ( 1247) hydrogen bonds : angle 4.37048 ( 3558) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7350.30 seconds wall clock time: 125 minutes 52.59 seconds (7552.59 seconds total)